Mass Effect: Game of Cloaks and Daggers
by Wardude86
Summary: My shot at a Mass Effect fan fic. Set after the events of ME3, Shepard wakes up from a coma after two years and finds that the galaxy barely changed in his and the reapers absence. Now that he's back he has a job to do. Rated M to be safe for language and content.
1. Chapter 1

**A/n: This is a little something I came up with on how I would have my Shepard be after the events of Mass Effect 3. He is an Infiltrator, with the Colonist/survior backround. I don't really care for the whole paragon/renegade thing, but he would probably be a 60/40. **

**I do not own any of the characters or the setting.**

* * *

I sat there looking out at the void of space as the arms of the Citadel opened to let the Crucible to dock. I looked at Anderson, one of my closest friends. He had been my instructor when I joined the Navy. He had been there to support me after Akuze, he had been my commanding officer for countless missions. Anderson was there the day I had became a Spectre. He was like a second father to me since my parents were killed on Mindoir, I sometimes had to surpress the urge to call him dad. He was smiling, and I knew why, we had done it; The Reapers where finished.

"I'm proud of you Shepard," said Anderson as he closed his eyes.

The bright light of the Crucible charging the 'Catalyst' sent out a great bout of energy, killing the Reapers as it went, leaving their large metallic corpses behind, unmoving and dead. I felt the energy fill the control room the air seemed to fizz and pop with energy before the control panel exploded launching Anderson and I to the edge of the platform, I grabbed him as his body slid over the edge, the station exploding around us, it was then I noticed that life had already left his body, a smile still plastered on his face. I let go, tears running down my face as the control me exploded, and every thing went black.

* * *

"He's reacting to outside stimuli," said a familiar voice, female and filled with a tone that hinted that the mind behind it held a lot of wisdom.

"His brain wave patterns are off the charts," said a voice that wasn't so familiar, male. I opened my eyes to look around me, but I couldn't move. The light infront of my eyes burned, it was so bright. Then a silhouette of someone's head blocked out the light, my eyes focused and the form of a smiling Dr. Chakwas formed out of the silhouette.

"Welcome back Commander," she said in a happy tone.

"Where..." I rasped, my throat was so dry and even that single word exerted all of my energy.

"Huerta Memorial Hospital," Dr. Chakwas answered in a cooing tone as she brushed her hand on my forehead, I noticed another person to my left with a syringe who inserted it into my IV tube. "Now I know you have a lot of questions but they will be answered in due time, rest now Rick, you deserve it." And with that I felt my eyes close and darkness once again.

* * *

"Proper Barrier control is only obtainable with great mental and physical endurance," lectured Instructor Jacquelyn Naught of Grissam Academy as she watched her students running laps around the grounds. Grissam Academy was once an Alliance ran program for gifted military cadets, now turned into Council ran biotic, technological, and public security trade school. Jacquelyn, or Jack as she preferred to be called by her peers, was one of the senior instructors in the biotic department of the Academy. Her appearance was unorthodox in comparison to the other instructors, covered head to toe in tattoos, her hair held into a wolf's tail on the top and the sides of her head buzzed to show the tattoos on her scalp. Unlike the other instructors she wasn't ex-military or police. In fact she was quite the opposite, once one of the most wanted criminals in the galaxy. She wore the Grissam Academy instructor nylon sweats and jacket, which was quite different from her usual attire which usually consisted of scant clothing and leather. Though in the last two years since the destruction of the Reapers, she had started going to work in a more professional manner, though after she clocked off she'd head to the bar with Garrus and Tali in her usual attire. When she wore her uniform it gave her feeling of warmth and protection, it was the same type of Alliance blues her boy... the man she loved used to wear, Richard W. Shepherd. After the wave of energy that left the Citadel and destroyed the Reapers, they had recovered Richard's comatose body from the wreckage. Medical experts where astonished on how he could have survived the explosion, but that was what he did: survive. Like he did on Mindoir and Akuze, he survived, but hasn't woken up for the last 2 years.

Now Jack focused only on her students, though once every week she'd go to see him in the hospital. Every time expecting him to wake up, but it never came. Then the once a week became once a month, but after her last atempt at a relationship she had started going back. Everyone had gone their separate ways since that last battle, Garrus Vakarian had gotten a position as a Spectre, mostly he worked with C-Sec to stay close, since his fiancee Tali'Zorah vas Rannoch, who was the Quarian Ambassador to the Citadel. They where the ones closest in distance and would keep in touch on a regular basis. Every one else had gone their seperate ways, with out Shepherd to keep them close, though they would come to visit every so often.

The Bell sounded across the grounds, signaling the end of the day's classes. "Alright everyone gather round," signaled Jack towards her class, "I want you guys to keep up your physical training over the break, You guys are going to be gone a week, that's plenty of time to cause your strength and endurance to degrade. Once you get back we'll actually start on barrier controll, enjoy your break!" They all walked off the field towards the locker rooms in a group some of the students had questions that she answered, but then something caught her eye. Leaning on one of the supports for the bleachers was a certain Turian who's face was covered in scars. Jack finished told her students to meet her at her office later for any other questions and sent them on their way.

"Hey leatherface!" she waved as she walked up to Garrus, who had that cocky grin that he usually wears, "What brings the great Archangel to Grissom Academy?"

"I got some good news and some bad news," replied the smug Turian, he looked around them and took notice to they're alone, "The most dangerous man in the galaxy is back in action. And the good news..." He paused for effect.

"and?"

"He's your boyfriend."

* * *

I sat there on the edge of my bed looking out the window out into the Presidium, it was beautiful. The white buildings and gardens filled with people hustling and bustling over every day matters, only made available thanks to his and every soldier's effort in fighting the Reapers, and he got to see it, the aftermath, what he fought for: a future. It chewed me up on the inside, I had set out to do the impossible and I had achieved it, but for all it's worth I felt very much alone. Dr. Chakwas and the Council being the only familiar faces I had seen since I woke up, they had confirmed that I still held my Spectre status and asked if I would like to return to active duty when I was ready, I said "I'll think about it." I had time I still had to go through physical therapy and reorient myself with any new waves of tech that has come out in the last few years, as well as the political climate. That was three weeks ago. I knew I was going to be center stage soon enough, though right now my recovery is being kept under wraps, don't want the media crowding me when I'm still recovering.

I looked down at my feet, they were so boney. I was as skinny as a tooth pick, once one of the most lethal assassain turned hero, barely able to sit up on my own. "Third time's the charm." I muttered before sliding off the bed onto my feet, which my legs responded by turning into jelly as I collapsed onto the floor. "Damn it." I cursed as I used my arms to turn myself over onto my back. 'On your feet Shepherd, there's work to be done,' sounded Anderson's voice in my head. I looked over and saw a wheeled tray and used it as a support to stand myself up, as I got onto my feet the tray rolled away from me and I went crashing down to the floor again.

"FUCK!" I yelled, slamming my fist on the floor, I hated being this helpless. Life was always going to shit on you no matter what so I have to be ready for anything to come through those doors. In my life I had made a lot of enemies, though I was able to focus them on the Reapers, now there was nothing to keep them from coming after me. I also wanted out of here, to be out in the world, and to be with Jack... fuck. It's been two years, the last time I spoke to her was right before the assault on the space elevator on Earth, the last time I saw her in person was at Purgatory, where we danced and drank our worries away. She probably moved on, gotten together with some other guy, probably still teaching.

I turned over and looked at my hands, the hands of a killer who has withered away, in to a memory. I am Richard Warren Shepard, Savior of the Citadel, Champion of the Terminus, Defeater of the Reapers, the man with the blood of hundreds of thousands on his hands, and I was still alive. Just like on Mindoir, just like Akuze, I survived, when so many others can't say the same. I need to stand and live for them, maybe continue being a Spectre, or enter politics, I showed that I was pretty good at it despite hating every moment of it. But what ever I do, I need to first stand on my feet again. I turned over on to my belly and combat crawled towards the window. I put out my hand and slowly used the window as a support. I slowly rose to my knees, then up on to on foot, then the other. I was in a crouch, then I slowly rose using the glass as a support. Once a full height I took a step back and lowered my hands to my sides and stood for the first time in two years.

Then I heard the door to the room open behind me open. "Rick?"

"Jack?" My stomach felt like it had a dozen butterflies fluttering about, I turned my head and it was indeed her, I smiled at her before the world blacked out once again.

When I came to I realized I had been strapped to the bed apparently Dr. Chakwas was tired of my shit. There was someone clenching onto my hand and I realized it was Jack. She was asleep in the room's visitor chair with her head resting on the side of the bed. I realized that the lights in the presidium had been turned off to simulate night. Probably pretty late I probably shouldn't wake her.

"Don't you dare leave me..." she mumbled in her sleep, clenching tighter on my hand, cute... "fucker..." And that is the Jack I fell in love with, and

"Or at least I hope she still is..." I muttered to myself turning to look out the window, and drifted back to sleep.

* * *

"56... 57... 58... 59...60... 61... 62..." counting with every push up I did, Dr. Chakwas was impressed with my sudden recovery. It was probably mostly due to the extensive gene modification I had received from Project Lazarus, from Cerberus, from the Illusive Man... I owed my living to see this day to that sad man. In the end he only fell into the same trap as Saren did years ago. Why did I feel so anxious? The Reapers are gone, what else is there for me to do?

"Today, Binary Helix has declared that they will be buying out..." Continued the news coverage on the main holoplayer in the room.

"86... 87... 88... 89..." I continued to exercise. That was it, the galaxy will continue on has it had before, this time with out the threat of the Reapers rearing their ugly heads. Now that the threat was gone, yes a lot of things did happen for the better, like the revitalization the Krogan species or the cooperation of the Quarians and the Geth as examples. The galaxy still needed a hero, to save it from itself. He could be that hero, he was what ever the galaxy needed him to be. A soldier, an assassain, a terrorist, a criminal, a spy... he couldn't see himself sitting down anytime soon ,he wanted to help shape the galaxy, but it had continued without him.

The door to the room opened and I heard the familiar voice of the second best shot in the galaxy, "Well if it isn't the famous Commander Shepard, still always getting ready for a fight, just like old times," Garrus had a look in his eye like he was deep in memories, "You've built up quite a reputation amongst the other Spectres, a lot have taken noticed to your recovery, me included."

"Heh, thought you would've made it someday," I chuckled as I rose onto my knees and sat on the ground, "but didn't you say you were going to sit back and live off the royalties off the vids?"

"Tali's idea, I was getting a little restless after sitting at home all day, every day. Something about cracking and going into a Vigilante rage, and if it did happen actually have some sort of authority to back me up," answered Garrus ending with a smirk, " I called up my father and Primarch Victus to pull some strings and here I am, a full-fledged Spectre, been mostly working on cleaning up the Citadel, much easier to do with out all the 'red tape.'" He made little qoutes with his fingers around the end there. "Though I'm more worried about you. I heard that they were going to reinstate you, but you're not going back to the Alliance, only working for the Council. What does Jack think about all this?"

I looked at the ground at that mention of Jack, "I haven't told her yet. I don't know what to tell her anymore Garrus. She's changed."

"She's been through a lot in the last two years, we all have," Garrus sat down on the bed and frowned, "but she's still Jack, she's been by your side more then anyone while you were in that coma. Yeah she tried moving on but she was always brought back here, to you. But anyways enough about women, I got a present for you from both Tali and I." Garrus pulled over a one foot by two foot box from the side of the bed behind him, and gave it to me. I opened it and it was a Kukri knife, I smiled, it looked just like the one I had on Akuze, that knife saved my life more then once, but I had lost it when the Collectors had destroyed the first Normandy. He had to make do with just a standard issue combat knife since then, well until the destruction of the Reapers. "I remember whenever we had to go through a jungle,and how you always where complaining about how you can't stab a bush out of your way, or get deep enough to fully slit a krogan's throat..."

"Thanks," I said as I stood and put the knife underneath my pillow, "Glad you remembered."

"Rick, be careful."

"Don't I always?"

"Just like old times indeed."

* * *

** Ending note: yes this may seem a little raw but it might change after I get the story going since I'm really only doing this as practice for my creative writing. Please read and review, I'd like to hear some feed back.**

**Peace out,  
**

**War.  
**


	2. Chapter 2

**A/N So I've always liked in Mass Effect 3 the melee attacks after sneaking around, which I got really good at on the multiplayer with. So I always figured that my Shepard was a Martial arts expert as well as a marksman. So I was thinking of a martial arts style, and then I saw _The Raid: Redemption _and decided that he learned that specific style. If you don't know what Silat is, just go watch The Raid.**

* * *

"Again!" yelled the tiny little Indonesian man, arms at his side, legs shoulder width apart. I spat the blood out of my mouth and charged him again using my elbow to try and stun him, he blocked that, which I knew and followed with a knee. He side stepped and punched me in the gut all of the air in my lungs escaping me. "You will never be a master of Silat, at this rate you will never bring vengeance on those who stole everything from you. To protect what is rightfully yours. To shield the innocent. To survive." We continued to tussle on the dojo floor.

"I decided... I'm signing up with the Alliance." I said brusied and battered on the mat, my teacher gave me a water bottle and sat down next to me.

"You will meet many hardships, Rick. The Alliance life will be hard, there will be a time where you will have to choose wither your duty or your feelings," said the old man, "Do not do something do something you will regret later."

"Don't worry I'll make you proud Rama," I replied.

"No, make yourself proud."

* * *

I woke up to the lights of the Presidium activating it's day time hours. That dream again, I had been having it a lot, recently. My martial arts teacher from high school, he had died of a heart attack shortly before the whole Saren debacle. I wish he was there for my Spectre inauguration, the man who took me under his wing after my parents were killed on Mindoir. He was a childhood friend of my father, and was more like an uncle to me. He was there for my graduation from High school, basic, and N7 training. He was the first person, besides Anderson, to come visit me in the hospital after I was recovered from Akuze, we grew distant after that. I was constantly busy and so was he as a Police commissioner on Earth. Then he died, and I didn't find out til I was on my way to Noveria, two weeks after the funeral.

I sat up and put on my civvies, today was the day I checked out Jack was probably on her way over to come pick me up. I put on a pair of slacks on and a button up shirt, rolled up the sleeves. I then sat down and read my emails still shuffling through all the fan mail, that was mostly dated to be about 2 years old. I was finally given the okay to send the replies out only a week ago. Apparently the media took notice of this, So my admission from the hospital will more then likely be a little hectic, 'I hope Jack has learned to keep patient over the last two years...'

About 30 minutes into my emails, I heard the door open up, "Hey Boy Scout! Time to get going." I smirked as I looked up from my Omni-tool, she was in black cargo and a spaghetti strap black tank. Her skin cover in tattoos save for her face, which held a feral beauty all in its own. If you where to ask me what an Amazonian warrior from the greek myths looked like I would show you a picture of her, Jack. My love and my life.

"But I was finally getting comfortable, warm meals, soft bed," she seemed to smile at that, but it had turned into a sneer, 'same old Jack.'

"Get up," she glowed blue and kicked the bed over, which in itself is no small feat. I had found myself on the floor coughing, saliva had gone down the wrong tube. Then she was on top of me, her arm glowing blue over my head. "You're coming with me whether you like it or not," she said with a smug smile.

"I go where I want..." I had my kukri knife to her stomach the foot long blade had already torn a hole in her shirt and a thin drop of blood trinkled down the blade. Her eyes had darted to the sudden pain, the looked up with a face of longing, he knew this kind of play turned her on. "...with who I want, luckily your on that list." and with that I dropped the blade and we kissed. She had started unbuttoning my shirt when we both heard the kind Dr. Chakwas politely cough.

The doctor was standing at the door with an annoyed look, "You're going to be late for your meeting with council remember." Chakwas then motioned in a Krogan orderly into the room, he had a black-eye from when he woke me up two days prior, he came in and picked up the bead with ease. "Now don't give Grac any more trouble and leave," she said with a smile and came over and gave us a hand to get up.

Jack gotten up on her own and scoffed, then her face became softer. "Yeah... Sorry, I got a little carried away." she said as I took Chakwas's hand mostly for balance, since I probably weighed twice, if not thrice, her weight.

"Hey, don't worry about it," I said as I dusted off my slacks, and shirt. 'Apologetic Jack? This could be interesting,' I thought as I reached out and pulled her into a hug, the whispered into Jack's ear, "once we're done here in the Presidium, we can find the darkest little rat whole and I'll give you that lay I owe ya."

"I'll have to hold you to it, but you got a Krogan burning a hole in your back," chuckled Jack in a hushed whisper with a kiss. With that I let her go and turned around

"Shepard..." the look in his eye, I had seen it in a lot of Krogan, the proud race that they are.

"Grac..." I returned the glare, the Krogan 'harrumphed' in response.

"Here take this, surprised you humans have a knife that can cut that deep," Grac held out my knife, handle first, "take care Shepard, if it wasn't for you I wouldn't have a family."

"Will do, and thanks," I said, which he responded with a nod and left the room. I looked at Jack and shrugged, she gave that lop-sided smirk at me that I loved so much, and walked out the room with me hot on her heels. I had to jog to catch up and placed my arm around her, I felt her tense up and then relax.

"Fucker..." she muttered under her breathe and socked me in the rib, I grunted with a smile of success because she didn't back away. We walked together into the main lobby which looked to have a group of reporters huddled at the main desk.

"Commander Shepard, a word!" yelled one reporter that had spotted him and Jack. I sighed and placed my head on my forehead, and could feel Jack tense up under my arm, she didn't like cameras. I don't blame her, they never lie but can be manipulated to any one's point of view. Plus I hated being seen. I preferred the darkness, where you can disappear at a moments notice, and Jack felt the same way. So I just walked forward my eyes fixed on that elevator to get out, to freedom. The reporters frantic questions, then I saw Khalisah al-Jilani, and smirked as she stepped right in front of me.

"Commander Shepard, would you like to schedule an interview?" she asked, I noticed that she didn't have her camera drone buzzing about. She didn't try to stop me instead walked with me towards the elevator.

"Now that's the most sensible request I got from the media today," I replied with a laugh, "send me an email, and I'll let you know when I'm available."

We had reached the elevator, and she turned and practically had to yell at us as we entered the elevator, "Will do, and thank you, smear jobs never had as good of ratings as actual news." It almost seemed like she was trying to hold every one back but I could have been imagining things. I looked down at Jack, she seemed to be spaced out she put her arms around me, and we stood there in silence.

The elevator doors opened and we walk out on to the Presidium walkways, "You okay?" I asked.

"Ye... no... shit it's complicated..." she mumbled, "I feel like this is a dream, and that I might wake up from it."

"Hey you're not getting all sentimental on me are you?" I chuckled, but she didn't respond, she only held me tighter. I stopped walking and embraced her, her head laying on my chest, "What's wrong?"

She only responded with a 'sniff.'

'God damn it, I added to her issues,' I cursed to myself. "Hey, about last night..."

"I know," she said, "If you feel like you need to play hero, go ahead," she said in a low hushed tone.

"Hey look at the bright side, no Collectors chasing us, no Reapers chasing us, heck no Cerberus is chasing us," I chuckled as I kissed her forehead, which she responded by looking up at me and looking me in the eye. Hazel met blue, she was worried, "Hey I won't be going on any missions until after the media coverage dies down, so I'll be here with you for the next couple of months."

She rose to kiss me and I lowered my head to meet her. We held there until we both had to part to draw breathe. "You should have taken up my offer to become a space pirate," she whispered into my ear.

"Yeah sometimes I wish I did too."

* * *

The main council hall looked just like it did four years ago, before this whole reaper business ever started, and he was glad to see the familiar faces on the council. Tevos, the asari councilor; Valern, of the Salarian Union; and Sparatus, of the Turian Hierarchy. Then the human representative I didn't recognize, a Hispanic man in what looked to be his mid 60s.

"Agent Shepard, it's good to see you in top health," started Sparatus, interrupting the debate they had been going over, "I'm sorry to hear that you where discharged from the Alliance Navy, though it was on honorable terms."

"Indeed, though he has denied our request to reinstate...," stated the human councilor.

"I'm a galaxy man," I interrupted the councilor, "I feel in order for me to fulfill my role as a Spectre I need to seperate from the Alliance's chain of command, though it would be an honor if you were to sponsor me. But I'm guessing this is not why I'm here."

"This is true," started Travos, "The council has deemed that any missions and investigations that require your attention be put on hold, at least until the media attention has died down, publicly."

"We need you to investigate the activities of Kassa Fabrication and Genex Chemical," continued Councilor Valern, "we believe they are trying to piece together the remaining factions of Cerberus together."

I frowned at that. "So you want me to sneak in to their headquarters?"

"Yes but your fame, might make this easier as well as more difficult," stated the human councilor.

"You'll more then likely receive an invitation to their big partnership party that will be held in the pent house of Kassa Fabrication's headquarters in the Local System on the new Mars Colony," continued Sparatus, "They'll want to sponser you and your Spectre activity, let them think that they have you and figure out any information about Cerberus and their activities."

"I accept the mission, but I have one request."

"And that would be?"

"I'm going to need a ship, I want the Normandy back."

* * *

**A/n: Yeah more conversation chapter, I'm trying to set things up and trying to not be as scattered with the chapter. Well tell me what you guys think, I'll take any support I can get.**

**Peace out,  
**

**War.  
**


End file.
